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Healthy Apple Cobbler Muffins

~ Comforting, delicious apple cobbler in a portable muffin! Bursting with apple flavor under a decadently crunchy cobbler topping. They’re really healthy and freeze great. And, we’ve even got make-ahead tips for you, too! ~

This Recipe Is:     Freezable    Make Ahead    Vegetarian  

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Apple cobbler. *Sigh*  So warm and comforting. Like fall is wrapping you in a giant bear hug.

But apple cobbler as a grab-and-go snack? Or for breakfast as you dash out the door on a busy morning? Unheard of! (That’d be one super-sloppy bear hug!)

Enter the Apple Cobbler Muffin: Bursting with apple flavors and fall spices, then studded with a satisfying, crunchy-craggy cobbler topping.

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It. Is. So. Good.

A bear hug for the uber-busy, let’s say. (And aren’t the uber-busy really the people most in need of a good bear hug, anyway!?!?)

If you know us, then you know we tested and re-tested our recipe until we found the exact right balance of apple flavors, the perfect amounts of spices, and just the right texture (as in: soft, pillowy muffin meets nutty-crisp topping … ahhhhhh …).

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Plus, we jam-crammed in tons of great nutrition with whole-wheat flour and oats, protein from two eggs and those yummy walnuts, and LOADS of healthy apples. (Apple four ways, seriously – two kinds of apples, plus apple juice and apple sauce. One of these a day should keep the doctor away for eons!)

But wait … it gets even better! These really are muffins for the uber-busy, for all of you who think you don’t have time to bake homemade muffins. We’ve worked all the angles!

No need to complete the entire prep and baking process all at once! You can get everything ready the night before you’re gonna bake, or even earlier in the day. So easy! Here’s how:

Make-Ahead Tips

  • Prepare the large bowl of dry ingredients, then wrap it in plastic and set it aside on the counter.
  • The bowl of wet ingredients … wrap and stash it in the fridge.

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  • You can even pre-shred the apples, then wrap them and store them in the fridge, too. They’ll turn a bit brown, of course, but that won’t affect the final delicious flavor a bit!

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  • Lastly, you can even toss together the cobbler topping ahead of time. For the very best results, we recommend that you don’t mix in the topping’s apple sauce and butter until you’re ready to bake the muffins. But, honestly, you really can mix the entire cobbler topping together and keep it wrapped in the fridge, too. We’ve tried it and can tell you it really turns out almost as good!

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  • When you’re ready to bake, just mix all the ingredients together! 

Oh – and the ultimate make-ahead tip? These freeze great! (So, make a double batch while you’re at it!) Once they’ve cooled completely, package them individually in plastic wrap and then seal them in freezer bags. Air is the enemy that will lead to freezer burn, so try to wrap them tightly and remove as much air as you can.

Recipe Tips

Just a couple quick tips and you’ll be ready to start:

  • As with most of our muffins, these perform beautifully when baked in foil muffin liners. Sure, you can use regular paper liners, but the muffins won’t release quite as easily, especially on the first day. For the perfect balance of non-stick style (’cause who doesn’t love a stylish muffin, right?!?!), look for patterned muffin cups that have an inner foil lining like the ones we used for photographing this post.

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  • After trying various combinations (including zucchini!), we fell in love with a mixture of half Granny Smith apple (so tart and refreshing!) and half Pink Lady (for sweetness). Use what you have on hand or what’s available at your local markets or orchards. There will be differences in flavor and texture depending on which apples you choose, but these are so good that the most important thing is just to hurry up and make them! (Now!)
  • Oh – and all that cinnamon? Yup. We monkeyed with the cinnamon and ginger (as well as cardamom and nutmeg, which didn’t make the cut!) until the flavor was exactly where we wanted it. Trust us – don’t skimp on the cinnamon!

The perfect, healthy, satisfying solution for busy-morning breakfasts and on-the-go snacks. It’s a cobbler … and it’s a big bear hug … all wrapped up in a delicious muffin …

Oh – and want more yummy hugs? Check out some of our other healthy and delicious muffin recipes, like our Healthy Double Chocolate Muffins with Fresh Strawberries, our Healthy Pumpkin-Chocolate Chip Muffins, our Praline Peach Muffins, or our Blueberry-White Chocolate Muffins!

Ahhhhh … fall in Ohio. We love the weekends spent with our families in the cooler temps amid the gorgeous autumn colors! Hiking in the parks nearby, laughing our way through corn mazes, choosing just the right pumpkin at a local farm, and cheering at kids’ soccer games. Oh – and apples! Lots of apples! Apple picking, apple cider … apples, apples, apples!

Our Facebook fans might’ve already seen these photos, but we seriously can’t get enough apples this season! We’ve had such fabulous and delicious trips to our local orchards!
Healthy Apple Cobbler Muffins

Healthy Apple Cobbler Muffins

Yield: 18 muffins
Prep Time: 20 minutes
Cook Time: 15 minutes
Total Time: 35 minutes

Comforting, delicious apple cobbler ... in a portable muffin! Bursting with apple flavor under a crunchy cobbler topping!

  Freezable  •  Make Ahead    Vegetarian  



  • 1 cup whole wheat flour
  • 1 cup unbleached, all-purpose flour
  • 4 teaspoons cinnamon
  • 1 teaspoon salt
  • 1 teaspoon baking powder
  • 1/2 teaspoon baking soda
  • 1/2 teaspoon ground ginger


  • 2 eggs, lightly beaten
  • 3/4 cup packed dark brown sugar
  • 1/2 cup unsweetened applesauce
  • 1/4 cup apple juice (or apple cider)
  • 1 tablespoon canola oil
  • 2 teaspoons vanilla


  • 2/3 cup quick oats
  • 1/2 cup chopped walnuts
  • 1/3 cup packed dark brown sugar
  • 1 1/2 - 2 tablespoons unsweetened applesauce
  • 1 tablespoon butter
  • 1 teaspoon cinnamon


  • 1 1/2 cups peeled, shredded Pink Lady apples or other sweet-tart apples (from 1-2 apples)
  • 1 1/2 cups peeled, shredded Granny Smith apples (from 1-2 apples)


  1. Preheat oven to 400°F. Line muffin pans with 18 foil liners.
  2. In a large bowl, combine all dry ingredients and stir well with a whisk until evenly combined.
  3. In a medium bowl, combine wet ingredients and whisk thoroughly.
  4. In another medium bowl, mix cobbler toppings, cutting in the applesauce and butter (the easiest way is with your fingers) until evenly distributed.
  5. Mix wet ingredients into the dry ingredients, stirring just to combine and being careful not to overmix. Add the shredded apples to the batter and stir again briefly, just to combine.
  6. Spoon batter into prepared muffin liners, filling each about 3/4 full.
  7. Divide the cobbler topping evenly, about 1 heaping tablespoon per muffin.
  8. Bake for 15-18 minutes or until a toothpick comes out clean.
  9. Cool in the pans for about 5 minutes or until the muffins are beginning to set and are cool enough to handle. Remove the muffins to wire racks to cool completely.


Make-ahead tips: The wet ingredients, dry ingredients, shredded apples, and cobbler topping can all be prepared and kept in separate plastic-wrapped bowls in the fridge (the dry ingredients on the counter) until you are ready to combine everything together and bake. For best results, however, we recommend that you don't mix the applesauce and butter into the cobbler topping until the last minute.

Freezing: These freeze beautifully (so you may want to make a double batch!). To freeze, wrap individually and store in freezer bags. They will thaw in about 45 minutes or, after removing foil liner, they can be gently defrosted at 50% power in the microwave in about 50-60 seconds.

Nutrition Information:
Yield: 18 servings Serving Size: 1 muffin
Amount Per Serving: Calories: 160Total Fat: 5gSaturated Fat: 1gTrans Fat: 0gUnsaturated Fat: 3gCholesterol: 22mgSodium: 203mgCarbohydrates: 28gFiber: 2gSugar: 14gProtein: 3g

Nutrition information should be considered an estimate only, and may vary depending on your choice of ingredients or preparation. No guarantees are made regarding allergies or dietary needs. Always consult a physician or dietician for specific advice and questions.

Did You Make This Recipe?

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  1. Looks amazing! I eat gluten free, could I sub a gluten free flour mix for the whole wheat and all purpose flour?

    1. Hi Kris! I have to be totally honest – I don’t have a lot of experience with subbing in gluten free flour mixes, so I can’t give you much firsthand advice here. My guess is that it will probably work, but without knowing exactly which brand of flour mix you’ll use (there is some variation in the ingredients and how they behave in baking applications) and without trying it personally, I can’t 100% guarantee success on your first try. I did find a couple of articles that might help you, though. Check out https://www.myrecipes.com/healthy-diet/baking-with-gluten-free-flour and https://blog.kingarthurflour.com/2015/02/20/making-recipe-gluten-free/. I hope that helps you some! And if you do give it a try – I’d love to know what brand you selected and how it worked for you, and I’m sure other readers who need to bake gluten free would value your input! ~Shelley

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